Matrix-dependent a/x pair and overdegraded w/y/z ions generated by radical-directed dissociation of peptide radical cations [M]⁺ in matrix-assisted laser desorption/ionization in-source decay

Fragmentation of peptide radical cations [M]^{. +} has been examined using matrix-assisted laser desorption/ionization (MALDI) in-source decay (ISD) with hydrogen-abstracting nitro-substituted matrices. The ISD spectra of peptides containing an arginine (Arg) residue at carboxyl (C)-termini showed preferential [w]⁺ ions when 4-nitro-1-naphthol (4,1-NNL) matrix was used, whereas the use of 3,5-dinitrosalicylic acid (3,5-DNSA) resulted in preferential [x]⁺ ions. Minor or some [d]⁺ , [x]⁺ , [y]⁺ , and [z]⁺ ions were also observed. For peptides containing Arg residue at amino (N)-termini, the ISD spectra showed preferential [a]⁺ ions independent of matrix used. The observed [a]⁺ , [w]⁺ , [x]⁺ , [y]⁺ , and [z]⁺ ions can be rationally explained by radical-directed dissociation (RDD) of the peptide radical cations [M]^{. +} , although [d]⁺ ions may be formed via Norrish Type I cleavage and/or by RDD of [M]^{. +} ions. The formation of overdegraded [d]⁺ , [w]⁺ , [y]⁺ , and [z]⁺ ions is discussed from the standpoint of the internal energy of radical cations [M]^{. +} and radical fragment ions [a + H]^{. +} and [x + H]^{. +} deposited via collisional interactions with excited matrix molecules in the MALDI plume. The radical site of the peptide cations [M]^{. +} was presumed to be backbone amide nitrogen, from MALDI-ISD data with three different deuterated amino acids.